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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.18 (56ae09e)

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-12-14, 17:16 PST based on data in:


        General Statistics

        Showing 166/166 rows and 3/6 columns.
        Sample Name% Dups% GCM Seqs
        Surface_26_S26_R1_001
        95.3%
        55%
        10.6
        Surface_26_S26_R2_001
        93.5%
        55%
        10.6
        Surface_27_S27_R1_001
        96.2%
        55%
        13.1
        Surface_27_S27_R2_001
        92.5%
        55%
        13.1
        Surface_28_S28_R1_001
        96.7%
        56%
        13.9
        Surface_28_S28_R2_001
        94.6%
        55%
        13.9
        Surface_29_S29_R1_001
        95.6%
        55%
        9.3
        Surface_29_S29_R2_001
        93.7%
        55%
        9.3
        Surface_55_S55_R1_001
        96.0%
        57%
        14.7
        Surface_55_S55_R2_001
        93.9%
        56%
        14.7
        Surface_56_S56_R1_001
        95.8%
        57%
        12.0
        Surface_56_S56_R2_001
        93.5%
        58%
        12.0
        Surface_57_S57_R1_001
        95.9%
        55%
        9.3
        Surface_57_S57_R2_001
        92.3%
        56%
        9.3
        Surface_58_S58_R1_001
        96.3%
        55%
        11.9
        Surface_58_S58_R2_001
        93.2%
        55%
        11.9
        Surface_81_S81_R1_001
        94.5%
        55%
        7.4
        Surface_81_S81_R2_001
        93.5%
        55%
        7.4
        Surface_82_S82_R1_001
        95.7%
        58%
        8.8
        Surface_82_S82_R2_001
        94.3%
        58%
        8.8
        Surface_83_S83_R1_001
        95.7%
        59%
        9.0
        Surface_83_S83_R2_001
        94.3%
        60%
        9.0
        nontreated_1_S1_R1_001
        96.5%
        56%
        19.6
        nontreated_1_S1_R2_001
        93.2%
        56%
        19.6
        nontreated_30_S30_R1_001
        96.1%
        56%
        13.8
        nontreated_30_S30_R2_001
        92.7%
        56%
        13.8
        pH55_2_S2_R1_001
        95.4%
        57%
        13.6
        pH55_2_S2_R2_001
        92.4%
        56%
        13.6
        pH55_31_S31_R1_001
        95.9%
        56%
        14.5
        pH55_31_S31_R2_001
        94.8%
        57%
        14.5
        pH55_32_S32_R1_001
        96.1%
        56%
        13.6
        pH55_32_S32_R2_001
        93.4%
        57%
        13.6
        pH55_33_S33_R1_001
        95.8%
        59%
        13.5
        pH55_33_S33_R2_001
        95.4%
        58%
        13.5
        pH55_34_S34_R1_001
        96.6%
        59%
        13.5
        pH55_34_S34_R2_001
        94.9%
        57%
        13.5
        pH55_3_S3_R1_001
        96.2%
        58%
        15.9
        pH55_3_S3_R2_001
        94.4%
        57%
        15.9
        pH55_4_S4_R1_001
        96.0%
        56%
        13.3
        pH55_4_S4_R2_001
        93.1%
        55%
        13.3
        pH55_59_S59_R1_001
        96.4%
        57%
        13.9
        pH55_59_S59_R2_001
        93.9%
        56%
        13.9
        pH55_5_S5_R1_001
        96.1%
        55%
        11.1
        pH55_5_S5_R2_001
        92.8%
        55%
        11.1
        pH55_60_S60_R1_001
        96.2%
        57%
        12.8
        pH55_60_S60_R2_001
        94.2%
        57%
        12.8
        pH55_61_S61_R1_001
        96.4%
        57%
        14.6
        pH55_61_S61_R2_001
        94.8%
        57%
        14.6
        pH55_62_S62_R1_001
        93.2%
        57%
        11.8
        pH55_62_S62_R2_001
        92.9%
        56%
        11.8
        pH55ogr_35_S35_R1_001
        94.9%
        56%
        10.4
        pH55ogr_35_S35_R2_001
        93.8%
        55%
        10.4
        pH55ogr_36_S36_R1_001
        96.2%
        57%
        14.2
        pH55ogr_36_S36_R2_001
        94.2%
        56%
        14.2
        pH55ogr_37_S37_R1_001
        96.7%
        58%
        15.5
        pH55ogr_37_S37_R2_001
        94.4%
        57%
        15.5
        pH55ogr_38_S38_R1_001
        96.3%
        56%
        12.0
        pH55ogr_38_S38_R2_001
        93.2%
        56%
        12.0
        pH55ogr_63_S63_R1_001
        96.2%
        58%
        14.3
        pH55ogr_63_S63_R2_001
        94.7%
        58%
        14.3
        pH55ogr_64_S64_R1_001
        95.8%
        56%
        16.9
        pH55ogr_64_S64_R2_001
        95.2%
        57%
        16.9
        pH55ogr_65_S65_R1_001
        94.8%
        56%
        7.2
        pH55ogr_65_S65_R2_001
        95.2%
        56%
        7.2
        pH55ogr_6_S6_R1_001
        96.4%
        56%
        19.6
        pH55ogr_6_S6_R2_001
        93.7%
        56%
        19.6
        pH55ogr_7_S7_R1_001
        96.2%
        56%
        12.9
        pH55ogr_7_S7_R2_001
        92.3%
        56%
        12.9
        pH55ogr_8_S8_R1_001
        95.4%
        55%
        11.5
        pH55ogr_8_S8_R2_001
        92.4%
        55%
        11.5
        pH55ogr_9_S9_R1_001
        95.0%
        57%
        8.8
        pH55ogr_9_S9_R2_001
        95.4%
        57%
        8.8
        pH65_18_S18_R1_001
        94.4%
        55%
        10.1
        pH65_18_S18_R2_001
        90.6%
        55%
        10.1
        pH65_19_S19_R1_001
        96.2%
        56%
        13.9
        pH65_19_S19_R2_001
        92.8%
        55%
        13.9
        pH65_20_S20_R1_001
        95.7%
        56%
        12.8
        pH65_20_S20_R2_001
        94.0%
        56%
        12.8
        pH65_21_S21_R1_001
        89.2%
        64%
        13.7
        pH65_21_S21_R2_001
        88.0%
        64%
        13.7
        pH65_47_S47_R1_001
        96.1%
        57%
        13.3
        pH65_47_S47_R2_001
        93.3%
        56%
        13.3
        pH65_48_S48_R1_001
        96.5%
        57%
        15.9
        pH65_48_S48_R2_001
        93.7%
        57%
        15.9
        pH65_49_S49_R1_001
        96.5%
        56%
        16.7
        pH65_49_S49_R2_001
        93.9%
        56%
        16.7
        pH65_50_S50_R1_001
        90.9%
        61%
        15.0
        pH65_50_S50_R2_001
        89.7%
        60%
        15.0
        pH65_73_S73_R1_001
        94.3%
        59%
        8.7
        pH65_73_S73_R2_001
        92.6%
        58%
        8.7
        pH65_74_S74_R1_001
        94.4%
        56%
        6.9
        pH65_74_S74_R2_001
        91.9%
        56%
        6.9
        pH65_75_S75_R1_001
        95.1%
        60%
        7.1
        pH65_75_S75_R2_001
        93.7%
        59%
        7.1
        pH65_76_S76_R1_001
        88.7%
        59%
        7.7
        pH65_76_S76_R2_001
        89.3%
        59%
        7.7
        pH65ogr_22_S22_R1_001
        95.5%
        55%
        9.8
        pH65ogr_22_S22_R2_001
        92.4%
        55%
        9.8
        pH65ogr_23_S23_R1_001
        96.3%
        57%
        12.9
        pH65ogr_23_S23_R2_001
        92.6%
        57%
        12.9
        pH65ogr_24_S24_R1_001
        95.2%
        57%
        10.9
        pH65ogr_24_S24_R2_001
        94.4%
        57%
        10.9
        pH65ogr_25_S25_R1_001
        91.9%
        60%
        13.1
        pH65ogr_25_S25_R2_001
        92.2%
        59%
        13.1
        pH65ogr_51_S51_R1_001
        96.5%
        57%
        15.2
        pH65ogr_51_S51_R2_001
        94.3%
        56%
        15.2
        pH65ogr_52_S52_R1_001
        96.4%
        56%
        12.6
        pH65ogr_52_S52_R2_001
        93.6%
        56%
        12.6
        pH65ogr_53_S53_R1_001
        95.4%
        56%
        11.1
        pH65ogr_53_S53_R2_001
        95.0%
        57%
        11.1
        pH65ogr_54_S54_R1_001
        95.2%
        56%
        15.3
        pH65ogr_54_S54_R2_001
        92.2%
        57%
        15.3
        pH65ogr_77_S77_R1_001
        95.4%
        55%
        6.7
        pH65ogr_77_S77_R2_001
        92.2%
        55%
        6.7
        pH65ogr_78_S78_R1_001
        95.2%
        56%
        7.3
        pH65ogr_78_S78_R2_001
        90.3%
        56%
        7.3
        pH65ogr_79_S79_R1_001
        95.7%
        56%
        8.5
        pH65ogr_79_S79_R2_001
        92.4%
        56%
        8.5
        pH65ogr_80_S80_R1_001
        93.1%
        57%
        7.2
        pH65ogr_80_S80_R2_001
        92.6%
        57%
        7.2
        pH6_10_S10_R1_001
        95.3%
        56%
        12.9
        pH6_10_S10_R2_001
        93.0%
        56%
        12.9
        pH6_11_S11_R1_001
        95.2%
        56%
        11.8
        pH6_11_S11_R2_001
        92.9%
        56%
        11.8
        pH6_12_S12_R1_001
        96.1%
        57%
        14.8
        pH6_12_S12_R2_001
        93.5%
        56%
        14.8
        pH6_13_S13_R1_001
        92.3%
        63%
        15.1
        pH6_13_S13_R2_001
        91.5%
        61%
        15.1
        pH6_39_S39_R1_001
        96.4%
        58%
        15.3
        pH6_39_S39_R2_001
        94.8%
        57%
        15.3
        pH6_40_S40_R1_001
        96.3%
        57%
        12.7
        pH6_40_S40_R2_001
        94.5%
        56%
        12.7
        pH6_41_S41_R1_001
        95.1%
        57%
        12.9
        pH6_41_S41_R2_001
        95.3%
        56%
        12.9
        pH6_42_S42_R1_001
        93.6%
        57%
        13.5
        pH6_42_S42_R2_001
        90.6%
        57%
        13.5
        pH6_66_S66_R1_001
        95.6%
        60%
        7.2
        pH6_66_S66_R2_001
        94.4%
        59%
        7.2
        pH6_67_S67_R1_001
        95.4%
        59%
        6.6
        pH6_67_S67_R2_001
        94.1%
        58%
        6.6
        pH6_68_S68_R1_001
        95.2%
        55%
        5.7
        pH6_68_S68_R2_001
        91.0%
        55%
        5.7
        pH6_69_S69_R1_001
        94.8%
        56%
        10.7
        pH6_69_S69_R2_001
        91.5%
        56%
        10.7
        pH6ogr_14_S14_R1_001
        95.7%
        55%
        12.3
        pH6ogr_14_S14_R2_001
        92.3%
        56%
        12.3
        pH6ogr_15_S15_R1_001
        95.2%
        56%
        12.3
        pH6ogr_15_S15_R2_001
        91.7%
        56%
        12.3
        pH6ogr_16_S16_R1_001
        96.3%
        56%
        14.0
        pH6ogr_16_S16_R2_001
        93.5%
        56%
        14.0
        pH6ogr_17_S17_R1_001
        95.8%
        55%
        10.0
        pH6ogr_17_S17_R2_001
        91.8%
        56%
        10.0
        pH6ogr_43_S43_R1_001
        95.5%
        57%
        12.8
        pH6ogr_43_S43_R2_001
        94.7%
        57%
        12.8
        pH6ogr_44_S44_R1_001
        96.2%
        57%
        12.3
        pH6ogr_44_S44_R2_001
        94.1%
        56%
        12.3
        pH6ogr_45_S45_R1_001
        95.7%
        56%
        10.9
        pH6ogr_45_S45_R2_001
        93.3%
        56%
        10.9
        pH6ogr_46_S46_R1_001
        96.8%
        57%
        12.9
        pH6ogr_46_S46_R2_001
        94.3%
        56%
        12.9
        pH6ogr_70_S70_R1_001
        95.5%
        56%
        7.6
        pH6ogr_70_S70_R2_001
        91.4%
        56%
        7.6
        pH6ogr_71_S71_R1_001
        95.6%
        57%
        8.3
        pH6ogr_71_S71_R2_001
        93.4%
        56%
        8.3
        pH6ogr_72_S72_R1_001
        96.4%
        56%
        7.9
        pH6ogr_72_S72_R2_001
        93.5%
        56%
        7.9

        Variant processing (accepted variants)

        This section contains statistics about whether called variants were retained for analysis or not. By default, variants are filtered out if they are not in the designed variants csv.

        loading..

        Variant processing (rejected variants)

        This section contains statistics about whether called variants were retained for analysis or not. By default, variants are filtered out if they are not in the designed variants csv.

        loading..

        Variant processing stats

        This section contains statistics about whether called variants were retained for analysis or not. By default, variants are filtered out if they are not in the designed variants csv.

        loading..

        GATK

        GATK is a toolkit offering a wide variety of tools with a primary focus on variant discovery and genotyping.DOI: 10.1101/201178; 10.1002/0471250953.bi1110s43; 10.1038/ng.806; 10.1101/gr.107524.110.

        GATK ASM counts

        Per-sample read count and base call fates from GATK AnalyzeSaturationMutagenesis.

        This table shows the distribution of calls (for reads or for bases) across all samples. Reads are categorized as WT, a variant, or filtered. Bases can be either evaluated or unevaluated, corresponding to the reads they come from.

        Reads are filtered for the following reasons:

        • Unmapped: the map quality is below the minimum MapQ (default = 4)'
        • Low quality reads: Reads are trimmed for quality > minQ (default 30) before calling variants. If the final size is less than the minimum length (default 15), or if the remaining segment does not cover the ORF, the read is filtered.

        Paired reads are also split into overlapping and disjoint sets, with further filters for both.

        • Inconsistent: If overlapping reads disagree on the called variant, the read is filtered.
        • Ignored mate: If the pairs are disjoint, the first read of the pair is used for analysis, and the second is ignored.
        • Low quality variation: If the variant includes ambiguous bases (not A, C, G, or T, or -), the read is filtered.
        • Insufficient flank: If the variant does not include a certain number of WT bases (default 2) flanking the variant, the read is filtered.
        Showing 83/83 rows and 4/22 columns.
        Sample NameTotal reads (M)WT reads (M)Variant reads (M)Filtered reads (M)
        nontreated_R1
        37.3
        14.9
        2.7
        7.6
        nontreated_R2
        26.5
        10.5
        1.8
        6.2
        ph55_R1_B1
        25.2
        10.1
        1.7
        5.6
        ph55_R1_B2
        29.4
        12.0
        2.0
        5.0
        ph55_R1_B3
        25.3
        10.2
        1.7
        5.9
        ph55_R1_B4
        21.0
        8.6
        1.3
        5.8
        ph55_R2_B1
        27.5
        11.0
        1.8
        6.0
        ph55_R2_B2
        26.0
        10.4
        1.8
        5.4
        ph55_R2_B3
        25.2
        10.3
        1.6
        3.6
        ph55_R2_B4
        25.3
        10.5
        1.5
        4.0
        ph55_R3_B1
        26.3
        10.7
        1.8
        5.8
        ph55_R3_B2
        24.2
        9.8
        1.6
        4.7
        ph55_R3_B3
        27.5
        11.3
        1.8
        4.9
        ph55_R3_B4
        21.3
        8.8
        1.2
        4.6
        ph55_ogr_R1_B1
        37.1
        14.8
        2.6
        8.0
        ph55_ogr_R1_B2
        24.6
        9.8
        1.7
        6.1
        ph55_ogr_R1_B3
        22.1
        8.7
        1.5
        5.9
        ph55_ogr_R1_B4
        16.6
        6.8
        1.0
        2.8
        ph55_ogr_R2_B1
        20.0
        7.9
        1.3
        5.0
        ph55_ogr_R2_B2
        26.9
        10.8
        1.9
        5.4
        ph55_ogr_R2_B3
        29.5
        12.0
        2.0
        5.3
        ph55_ogr_R2_B4
        23.2
        9.3
        1.5
        5.8
        ph55_ogr_R3_B1
        26.8
        10.9
        1.8
        4.4
        ph55_ogr_R3_B2
        32.0
        12.8
        2.0
        7.3
        ph55_ogr_R3_B4
        13.8
        5.7
        0.8
        3.1
        ph65_R1_B1
        19.5
        7.6
        1.1
        6.5
        ph65_R1_B2
        26.8
        10.7
        1.8
        7.0
        ph65_R1_B3
        24.4
        9.8
        1.6
        6.0
        ph65_R1_B4
        13.9
        5.9
        0.8
        0.8
        ph65_R2_B1
        25.2
        10.2
        1.7
        5.3
        ph65_R2_B2
        30.4
        12.2
        2.1
        6.2
        ph65_R2_B3
        31.8
        12.8
        2.2
        7.0
        ph65_R2_B4
        14.9
        6.2
        0.9
        2.0
        ph65_R3_B1
        14.5
        6.0
        0.9
        2.1
        ph65_R3_B2
        12.3
        5.0
        0.8
        2.9
        ph65_R3_B3
        12.5
        5.2
        0.8
        1.5
        ph65_R3_B4
        8.7
        3.6
        0.5
        1.4
        ph65_ogr_R1_B1
        18.7
        7.4
        1.3
        4.8
        ph65_ogr_R1_B2
        24.4
        9.8
        1.6
        4.7
        ph65_ogr_R1_B3
        20.7
        8.4
        1.3
        3.9
        ph65_ogr_R1_B4
        18.0
        7.5
        1.0
        2.4
        ph65_ogr_R2_B1
        28.8
        11.7
        2.0
        5.7
        ph65_ogr_R2_B2
        24.3
        9.7
        1.7
        5.5
        ph65_ogr_R2_B3
        21.3
        8.6
        1.3
        4.9
        ph65_ogr_R2_B4
        24.5
        10.2
        1.4
        5.5
        ph65_ogr_R3_B1
        13.0
        5.2
        0.9
        3.6
        ph65_ogr_R3_B2
        14.0
        5.6
        0.9
        3.6
        ph65_ogr_R3_B3
        16.3
        6.6
        1.1
        3.8
        ph65_ogr_R3_B4
        11.3
        4.7
        0.6
        2.0
        ph6_R1_B1
        24.6
        9.8
        1.6
        6.3
        ph6_R1_B2
        22.5
        8.9
        1.6
        5.3
        ph6_R1_B3
        28.1
        11.3
        1.9
        6.0
        ph6_R1_B4
        20.0
        8.4
        1.1
        1.7
        ph6_R2_B1
        28.8
        11.7
        1.9
        4.8
        ph6_R2_B2
        24.1
        9.7
        1.7
        4.8
        ph6_R2_B3
        24.4
        9.8
        1.4
        5.2
        ph6_R2_B4
        17.9
        7.5
        1.1
        3.8
        ph6_R3_B1
        13.1
        5.4
        0.8
        1.4
        ph6_R3_B2
        12.0
        5.0
        0.8
        1.6
        ph6_R3_B3
        11.1
        4.5
        0.7
        3.4
        ph6_R3_B4
        19.0
        7.6
        1.3
        4.6
        ph6_ogr_R1_B1
        23.5
        9.4
        1.6
        6.3
        ph6_ogr_R1_B2
        23.4
        9.2
        1.5
        5.9
        ph6_ogr_R1_B3
        26.7
        10.8
        1.9
        5.8
        ph6_ogr_R1_B4
        18.8
        7.7
        1.1
        5.1
        ph6_ogr_R2_B1
        24.3
        9.8
        1.6
        4.8
        ph6_ogr_R2_B2
        23.4
        9.4
        1.7
        4.6
        ph6_ogr_R2_B3
        20.9
        8.3
        1.4
        5.2
        ph6_ogr_R2_B4
        24.4
        10.1
        1.5
        5.1
        ph6_ogr_R3_B1
        14.6
        5.8
        1.0
        3.7
        ph6_ogr_R3_B3
        15.7
        6.4
        1.0
        3.4
        ph6_ogr_R3_B4
        15.2
        6.3
        0.9
        3.5
        surface_R1_B1
        20.3
        8.0
        1.4
        5.7
        surface_R1_B2
        25.3
        10.0
        1.8
        6.8
        surface_R1_B3
        26.8
        10.9
        1.7
        6.4
        surface_R1_B4
        17.7
        7.2
        1.0
        5.2
        surface_R2_B1
        27.7
        11.1
        1.9
        5.7
        surface_R2_B2
        22.8
        9.1
        1.6
        4.3
        surface_R2_B3
        17.8
        7.2
        1.2
        4.7
        surface_R2_B4
        22.8
        9.2
        1.4
        6.4
        surface_R3_B1
        14.2
        5.6
        0.9
        3.6
        surface_R3_B2
        16.4
        6.7
        1.1
        2.5
        surface_R3_B4
        16.5
        6.8
        1.0
        2.1

        Read counts

        Read counts and read fate. Filtered reads include unmapped, low quality, and other pathologies.

        Reads can be filtered by GATK AnalyzeSaturationMutagenesis for a number of reasons, including low quality, insufficient flank, and other pathologies. This plot shows the number of reads that were mapped to WT, called as variants, and the number that were filtered.

        loading..

        Base calls

        Base calls evaluated for variants and base calls not evaluated for variants.

        Bases can be filtered by GATK AnalyzeSaturationMutagenesis for a number of reasons, including low quality, insufficient flank, and other pathologies. This plot shows the number of base calls that were evaluated for variants and the number of base calls that were not evaluated for variants.

        loading..

        BBTools

        BBTools is a suite of fast multithreaded bioinformatics tools designed for the analysis of DNA and RNA sequence data.

        BBDuk filtering statistics summary table

        Proportion of reads that matched adapters/contaminants.

        Showing 83/83 rows and 1/3 columns.
        Sample NamePercent filtered
        nontreated_R1
        0.0%
        nontreated_R2
        23.0%
        ph55_R1_B1
        25.0%
        ph55_R1_B2
        0.0%
        ph55_R1_B3
        22.9%
        ph55_R1_B4
        16.8%
        ph55_R2_B1
        24.8%
        ph55_R2_B2
        0.0%
        ph55_R2_B3
        37.9%
        ph55_R2_B4
        33.4%
        ph55_R3_B1
        0.0%
        ph55_R3_B2
        0.0%
        ph55_R3_B3
        0.0%
        ph55_R3_B4
        0.0%
        ph55_ogr_R1_B1
        0.0%
        ph55_ogr_R1_B2
        21.4%
        ph55_ogr_R1_B3
        19.1%
        ph55_ogr_R1_B4
        31.6%
        ph55_ogr_R2_B1
        21.6%
        ph55_ogr_R2_B2
        0.0%
        ph55_ogr_R2_B3
        31.4%
        ph55_ogr_R2_B4
        20.5%
        ph55_ogr_R3_B1
        32.7%
        ph55_ogr_R3_B2
        0.0%
        ph55_ogr_R3_B4
        24.7%
        ph65_R1_B1
        14.0%
        ph65_R1_B2
        18.9%
        ph65_R1_B3
        21.8%
        ph65_R1_B4
        64.9%
        ph65_R2_B1
        26.5%
        ph65_R2_B2
        27.0%
        ph65_R2_B3
        24.6%
        ph65_R2_B4
        43.8%
        ph65_R3_B1
        39.3%
        ph65_R3_B2
        0.0%
        ph65_R3_B3
        0.0%
        ph65_R3_B4
        37.6%
        ph65_ogr_R1_B1
        19.5%
        ph65_ogr_R1_B2
        0.0%
        ph65_ogr_R1_B3
        29.2%
        ph65_ogr_R1_B4
        0.0%
        ph65_ogr_R2_B1
        28.3%
        ph65_ogr_R2_B2
        0.0%
        ph65_ogr_R2_B3
        24.0%
        ph65_ogr_R2_B4
        23.4%
        ph65_ogr_R3_B1
        16.8%
        ph65_ogr_R3_B2
        0.0%
        ph65_ogr_R3_B3
        22.4%
        ph65_ogr_R3_B4
        29.9%
        ph6_R1_B1
        21.1%
        ph6_R1_B2
        0.0%
        ph6_R1_B3
        25.8%
        ph6_R1_B4
        53.6%
        ph6_R2_B1
        33.4%
        ph6_R2_B2
        26.3%
        ph6_R2_B3
        27.6%
        ph6_R2_B4
        27.8%
        ph6_R3_B1
        44.8%
        ph6_R3_B2
        39.4%
        ph6_R3_B3
        14.3%
        ph6_R3_B4
        20.5%
        ph6_ogr_R1_B1
        18.9%
        ph6_ogr_R1_B2
        22.4%
        ph6_ogr_R1_B3
        24.1%
        ph6_ogr_R1_B4
        17.6%
        ph6_ogr_R2_B1
        0.0%
        ph6_ogr_R2_B2
        25.9%
        ph6_ogr_R2_B3
        0.0%
        ph6_ogr_R2_B4
        0.0%
        ph6_ogr_R3_B1
        20.3%
        ph6_ogr_R3_B3
        25.6%
        ph6_ogr_R3_B4
        22.4%
        surface_R1_B1
        16.3%
        surface_R1_B2
        17.3%
        surface_R1_B3
        0.0%
        surface_R1_B4
        0.0%
        surface_R2_B1
        26.9%
        surface_R2_B2
        0.0%
        surface_R2_B3
        18.9%
        surface_R2_B4
        17.2%
        surface_R3_B1
        20.0%
        surface_R3_B2
        34.5%
        surface_R3_B4
        41.7%

        Identity histogram

        Histogram of read count versus percent base pair identity of aligned reads (idhist).

        loading..

        Identity histogram summary table

        Histogram of read count versus percent base pair identity of aligned reads (idhist).

        Showing 83/83 rows and 8/8 columns.
        Sample NameMean_readsMean_basesMedian_readsMedian_basesMode_readsMode_basesSTDev_readsSTDev_bases
        nontreated_R1
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.5
        nontreated_R2
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.4
        7.5
        ph55_R1_B1
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.8
        ph55_R1_B2
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.8
        7.9
        ph55_R1_B3
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.3
        7.4
        ph55_R1_B4
        97.8
        97.8
        100.0
        100.0
        100.0
        100.0
        6.7
        6.8
        ph55_R2_B1
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph55_R2_B2
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.8
        7.9
        ph55_R2_B3
        97.4
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.8
        ph55_R2_B4
        97.8
        97.7
        100.0
        100.0
        100.0
        100.0
        6.8
        7.0
        ph55_R3_B1
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.8
        ph55_R3_B2
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.8
        ph55_R3_B3
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph55_R3_B4
        97.7
        97.7
        100.0
        100.0
        100.0
        100.0
        6.9
        7.0
        ph55_ogr_R1_B1
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.8
        7.8
        ph55_ogr_R1_B2
        97.2
        97.1
        100.0
        100.0
        100.0
        100.0
        7.9
        7.9
        ph55_ogr_R1_B3
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.4
        7.5
        ph55_ogr_R1_B4
        97.7
        97.6
        100.0
        100.0
        100.0
        100.0
        7.0
        7.1
        ph55_ogr_R2_B1
        97.2
        97.1
        100.0
        100.0
        100.0
        100.0
        7.8
        7.9
        ph55_ogr_R2_B2
        97.2
        97.1
        100.0
        100.0
        100.0
        100.0
        7.9
        8.0
        ph55_ogr_R2_B3
        97.4
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.8
        ph55_ogr_R2_B4
        97.7
        97.6
        100.0
        100.0
        100.0
        100.0
        6.8
        6.9
        ph55_ogr_R3_B1
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.8
        7.9
        ph55_ogr_R3_B2
        97.2
        97.2
        100.0
        100.0
        100.0
        100.0
        7.8
        7.9
        ph55_ogr_R3_B4
        97.8
        97.7
        100.0
        100.0
        100.0
        100.0
        6.8
        6.9
        ph65_R1_B1
        97.3
        97.3
        100.0
        100.0
        100.0
        100.0
        7.3
        7.3
        ph65_R1_B2
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.5
        ph65_R1_B3
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph65_R1_B4
        97.5
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        8.0
        ph65_R2_B1
        97.4
        97.4
        100.0
        100.0
        100.0
        100.0
        7.4
        7.5
        ph65_R2_B2
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.4
        7.5
        ph65_R2_B3
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph65_R2_B4
        97.5
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph65_R3_B1
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.4
        7.6
        ph65_R3_B2
        97.4
        97.4
        100.0
        100.0
        100.0
        100.0
        7.5
        7.5
        ph65_R3_B3
        97.5
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph65_R3_B4
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.9
        ph65_ogr_R1_B1
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.6
        ph65_ogr_R1_B2
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.6
        ph65_ogr_R1_B3
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.3
        7.4
        ph65_ogr_R1_B4
        97.8
        97.6
        100.0
        100.0
        100.0
        100.0
        6.9
        7.1
        ph65_ogr_R2_B1
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.6
        ph65_ogr_R2_B2
        97.3
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph65_ogr_R2_B3
        97.4
        97.4
        100.0
        100.0
        100.0
        100.0
        7.5
        7.6
        ph65_ogr_R2_B4
        97.8
        97.7
        100.0
        100.0
        100.0
        100.0
        6.9
        7.0
        ph65_ogr_R3_B1
        97.3
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.6
        ph65_ogr_R3_B2
        97.2
        97.2
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph65_ogr_R3_B3
        97.3
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph65_ogr_R3_B4
        97.7
        97.6
        100.0
        100.0
        100.0
        100.0
        7.1
        7.2
        ph6_R1_B1
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.4
        7.4
        ph6_R1_B2
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.5
        ph6_R1_B3
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.3
        7.4
        ph6_R1_B4
        97.7
        97.5
        100.0
        100.0
        100.0
        100.0
        7.2
        7.4
        ph6_R2_B1
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.5
        7.6
        ph6_R2_B2
        97.4
        97.4
        100.0
        100.0
        100.0
        100.0
        7.6
        7.6
        ph6_R2_B3
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph6_R2_B4
        97.8
        97.7
        100.0
        100.0
        100.0
        100.0
        6.9
        7.0
        ph6_R3_B1
        97.4
        97.2
        100.0
        100.0
        100.0
        100.0
        7.6
        7.8
        ph6_R3_B2
        97.5
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph6_R3_B3
        97.3
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.6
        ph6_R3_B4
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.3
        7.4
        ph6_ogr_R1_B1
        97.3
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.6
        ph6_ogr_R1_B2
        97.2
        97.2
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph6_ogr_R1_B3
        97.5
        97.4
        100.0
        100.0
        100.0
        100.0
        7.3
        7.4
        ph6_ogr_R1_B4
        97.7
        97.7
        100.0
        100.0
        100.0
        100.0
        6.9
        6.9
        ph6_ogr_R2_B1
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph6_ogr_R2_B2
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.8
        ph6_ogr_R2_B3
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.6
        ph6_ogr_R2_B4
        97.8
        97.8
        100.0
        100.0
        100.0
        100.0
        6.7
        6.8
        ph6_ogr_R3_B1
        97.2
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.8
        ph6_ogr_R3_B3
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        ph6_ogr_R3_B4
        97.7
        97.7
        100.0
        100.0
        100.0
        100.0
        6.9
        7.0
        surface_R1_B1
        97.2
        97.2
        100.0
        100.0
        100.0
        100.0
        7.8
        7.8
        surface_R1_B2
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.6
        7.7
        surface_R1_B3
        97.7
        97.7
        100.0
        100.0
        100.0
        100.0
        6.9
        7.0
        surface_R1_B4
        97.8
        97.8
        100.0
        100.0
        100.0
        100.0
        6.6
        6.7
        surface_R2_B1
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.8
        7.9
        surface_R2_B2
        97.4
        97.3
        100.0
        100.0
        100.0
        100.0
        7.5
        7.6
        surface_R2_B3
        97.6
        97.6
        100.0
        100.0
        100.0
        100.0
        7.0
        7.0
        surface_R2_B4
        97.7
        97.7
        100.0
        100.0
        100.0
        100.0
        6.7
        6.8
        surface_R3_B1
        97.2
        97.1
        100.0
        100.0
        100.0
        100.0
        7.9
        7.9
        surface_R3_B2
        97.3
        97.2
        100.0
        100.0
        100.0
        100.0
        7.7
        7.8
        surface_R3_B4
        97.7
        97.5
        100.0
        100.0
        100.0
        100.0
        7.0
        7.2

        Indel lengths

        Indel length histogram (indelhist). The plots show the number of observed insertions and deletions, for each insertion and deletion length.

        loading..

        Match, substitution, deletion, and insertion rates

        Histogram of match, substitution, deleletion, and insertion rates by read location (mhist).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Read quality

        Histogram of average read qualities (aqhist). Plot shows the number of reads at each quality score.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Errors-per-read

        Errors-per-read histogram (ehist).

        loading..

        Read lengths

        Read length histogram (lhist).

        loading..

        Insert sizes

        Histogram of computed insert sizes, for paired reads (ihist). Plotted data has been cut off at 99% to prevent long tails; Complete data available in original source files.

        The insert size is the length of the sequence between the sequencing adapters, which for most common insert sizes is longer than the sum of both read pairs. In some cases, the insert size is shorter than the length of the two read pairs combined, resulting in an insert size shorter than the sum of the length of the reads pairs.

        loading..

        Insert sizes summary table

        Histogram of computed insert sizes, for paired reads (ihist). Plotted data has been cut off at 99% to prevent long tails; Complete data available in original source files.

        The insert size is the length of the sequence between the sequencing adapters, which for most common insert sizes is longer than the sum of both read pairs. In some cases, the insert size is shorter than the length of the two read pairs combined, resulting in an insert size shorter than the sum of the length of the reads pairs.

        Showing 83/83 rows and 4/4 columns.
        Sample NameMeanMedianSTDevPercentOfPairs
        nontreated_R1
        160.0
        158.0
        68.7
        61.0
        nontreated_R2
        163.4
        163.0
        70.4
        55.6
        ph55_R1_B1
        160.2
        158.0
        70.4
        57.4
        ph55_R1_B2
        153.4
        148.0
        69.1
        67.9
        ph55_R1_B3
        162.2
        161.0
        69.5
        54.6
        ph55_R1_B4
        169.9
        171.0
        68.7
        45.1
        ph55_R2_B1
        162.1
        161.0
        69.5
        59.2
        ph55_R2_B2
        160.5
        159.0
        69.6
        60.2
        ph55_R2_B3
        148.4
        141.0
        69.1
        75.0
        ph55_R2_B4
        153.5
        149.0
        69.5
        70.7
        ph55_R3_B1
        160.4
        158.0
        70.5
        57.3
        ph55_R3_B2
        157.7
        155.0
        70.1
        63.4
        ph55_R3_B3
        153.5
        149.0
        70.6
        65.6
        ph55_R3_B4
        162.2
        161.0
        70.6
        59.9
        ph55_ogr_R1_B1
        159.4
        157.0
        69.1
        59.2
        ph55_ogr_R1_B2
        163.5
        162.0
        69.5
        51.8
        ph55_ogr_R1_B3
        167.1
        168.0
        69.5
        49.1
        ph55_ogr_R1_B4
        156.6
        153.0
        68.5
        70.2
        ph55_ogr_R2_B1
        164.5
        164.0
        70.0
        53.3
        ph55_ogr_R2_B2
        158.7
        156.0
        69.8
        61.7
        ph55_ogr_R2_B3
        153.2
        148.0
        69.5
        65.8
        ph55_ogr_R2_B4
        165.3
        166.0
        70.8
        50.8
        ph55_ogr_R3_B1
        153.9
        149.0
        69.6
        69.5
        ph55_ogr_R3_B2
        164.7
        164.0
        70.3
        57.0
        ph55_ogr_R3_B4
        161.1
        160.0
        70.5
        58.0
        ph65_R1_B1
        171.6
        174.0
        70.1
        38.2
        ph65_R1_B2
        167.8
        168.0
        69.3
        49.0
        ph65_R1_B3
        163.9
        163.0
        70.0
        53.1
        ph65_R1_B4
        117.0
        103.0
        62.1
        90.9
        ph65_R2_B1
        158.3
        156.0
        70.2
        59.7
        ph65_R2_B2
        158.2
        155.0
        70.5
        60.5
        ph65_R2_B3
        161.3
        160.0
        69.7
        58.0
        ph65_R2_B4
        140.3
        130.0
        69.9
        77.8
        ph65_R3_B1
        144.3
        136.0
        69.5
        73.5
        ph65_R3_B2
        166.5
        167.0
        69.4
        54.4
        ph65_R3_B3
        145.2
        137.0
        69.0
        78.5
        ph65_R3_B4
        146.6
        139.0
        69.8
        72.3
        ph65_ogr_R1_B1
        166.7
        167.0
        69.4
        49.7
        ph65_ogr_R1_B2
        155.7
        152.0
        69.5
        63.7
        ph65_ogr_R1_B3
        158.1
        155.0
        68.8
        66.0
        ph65_ogr_R1_B4
        142.8
        134.0
        68.4
        77.7
        ph65_ogr_R2_B1
        156.2
        152.0
        70.2
        61.8
        ph65_ogr_R2_B2
        167.3
        168.0
        69.4
        56.5
        ph65_ogr_R2_B3
        163.2
        162.0
        70.9
        57.7
        ph65_ogr_R2_B4
        163.1
        162.0
        70.9
        56.1
        ph65_ogr_R3_B1
        171.8
        174.0
        69.5
        46.1
        ph65_ogr_R3_B2
        166.0
        166.0
        70.0
        50.5
        ph65_ogr_R3_B3
        163.4
        162.0
        69.9
        54.2
        ph65_ogr_R3_B4
        157.8
        155.0
        69.3
        67.0
        ph6_R1_B1
        164.1
        164.0
        69.7
        51.8
        ph6_R1_B2
        163.8
        163.0
        69.2
        55.9
        ph6_R1_B3
        159.2
        157.0
        69.5
        58.8
        ph6_R1_B4
        131.3
        120.0
        65.2
        86.7
        ph6_R2_B1
        152.1
        147.0
        69.2
        69.2
        ph6_R2_B2
        161.0
        159.0
        69.2
        61.4
        ph6_R2_B3
        157.6
        155.0
        69.8
        61.6
        ph6_R2_B4
        155.7
        151.0
        70.6
        60.0
        ph6_R3_B1
        141.4
        132.0
        68.4
        81.5
        ph6_R3_B2
        146.2
        138.0
        69.8
        75.7
        ph6_R3_B3
        170.9
        173.0
        70.4
        38.4
        ph6_R3_B4
        167.2
        168.0
        70.2
        52.4
        ph6_ogr_R1_B1
        166.4
        167.0
        69.9
        47.7
        ph6_ogr_R1_B2
        162.4
        161.0
        69.3
        53.5
        ph6_ogr_R1_B3
        162.7
        162.0
        70.0
        57.6
        ph6_ogr_R1_B4
        167.8
        169.0
        69.8
        45.5
        ph6_ogr_R2_B1
        156.1
        152.0
        69.6
        63.7
        ph6_ogr_R2_B2
        161.6
        160.0
        69.6
        61.4
        ph6_ogr_R2_B3
        162.3
        161.0
        70.4
        52.8
        ph6_ogr_R2_B4
        158.1
        155.0
        69.8
        59.5
        ph6_ogr_R3_B1
        165.4
        165.0
        70.4
        50.2
        ph6_ogr_R3_B3
        159.5
        157.0
        69.8
        58.5
        ph6_ogr_R3_B4
        163.0
        162.0
        69.6
        54.2
        surface_R1_B1
        173.8
        177.0
        69.9
        46.2
        surface_R1_B2
        171.0
        173.0
        68.7
        47.2
        surface_R1_B3
        167.3
        168.0
        69.6
        53.3
        surface_R1_B4
        171.2
        173.0
        70.0
        43.0
        surface_R2_B1
        158.4
        156.0
        69.8
        60.8
        surface_R2_B2
        159.5
        157.0
        69.2
        64.3
        surface_R2_B3
        166.4
        167.0
        70.5
        47.7
        surface_R2_B4
        169.6
        171.0
        69.9
        45.6
        surface_R3_B1
        167.1
        168.0
        70.4
        51.3
        surface_R3_B2
        152.1
        147.0
        69.8
        71.3
        surface_R3_B4
        143.6
        135.0
        70.0
        77.4

        GC content

        Read GC content histogram (gchist).

        loading..

        GC content summary table

        Read GC content histogram (gchist).

        Showing 83/83 rows and 4/4 columns.
        Sample NameMeanMedianModeSTDev
        nontreated_R1
        56.8
        53.6
        52.4
        7.1
        nontreated_R2
        56.3
        53.4
        52.4
        6.8
        ph55_R1_B1
        57.0
        53.6
        52.4
        7.3
        ph55_R1_B2
        57.7
        54.2
        52.4
        7.6
        ph55_R1_B3
        56.3
        53.4
        52.4
        6.8
        ph55_R1_B4
        55.4
        53.0
        52.4
        6.1
        ph55_R2_B1
        56.9
        53.6
        52.4
        7.2
        ph55_R2_B2
        57.0
        53.6
        52.4
        7.2
        ph55_R2_B3
        59.0
        55.6
        52.4
        8.2
        ph55_R2_B4
        58.4
        54.8
        52.4
        8.1
        ph55_R3_B1
        56.9
        53.6
        52.4
        7.2
        ph55_R3_B2
        57.7
        54.2
        52.4
        7.7
        ph55_R3_B3
        57.5
        54.0
        52.4
        7.5
        ph55_R3_B4
        56.7
        53.6
        52.4
        7.1
        ph55_ogr_R1_B1
        56.8
        53.6
        52.4
        7.1
        ph55_ogr_R1_B2
        56.5
        53.4
        52.4
        7.0
        ph55_ogr_R1_B3
        56.0
        53.2
        52.4
        6.5
        ph55_ogr_R1_B4
        57.6
        54.2
        52.4
        7.5
        ph55_ogr_R2_B1
        56.2
        53.4
        52.4
        6.8
        ph55_ogr_R2_B2
        57.2
        53.8
        52.4
        7.4
        ph55_ogr_R2_B3
        58.1
        54.4
        52.4
        7.9
        ph55_ogr_R2_B4
        56.2
        53.2
        52.4
        6.8
        ph55_ogr_R3_B1
        58.3
        54.6
        52.4
        8.0
        ph55_ogr_R3_B2
        56.7
        53.6
        52.4
        7.2
        ph55_ogr_R3_B4
        56.6
        53.4
        52.4
        7.1
        ph65_R1_B1
        55.4
        53.2
        52.4
        6.1
        ph65_R1_B2
        55.9
        53.2
        52.4
        6.5
        ph65_R1_B3
        56.6
        53.4
        52.4
        7.0
        ph65_R1_B4
        64.8
        65.4
        52.4
        9.3
        ph65_R2_B1
        57.2
        53.8
        52.4
        7.5
        ph65_R2_B2
        57.3
        53.8
        52.4
        7.5
        ph65_R2_B3
        57.0
        53.6
        52.4
        7.3
        ph65_R2_B4
        61.0
        59.6
        52.4
        9.4
        ph65_R3_B1
        59.2
        56.2
        52.4
        8.4
        ph65_R3_B2
        56.6
        53.6
        52.4
        6.9
        ph65_R3_B3
        59.8
        57.0
        52.4
        8.5
        ph65_R3_B4
        59.4
        57.2
        52.4
        9.1
        ph65_ogr_R1_B1
        55.7
        53.2
        52.4
        6.3
        ph65_ogr_R1_B2
        57.7
        54.2
        52.4
        7.7
        ph65_ogr_R1_B3
        57.7
        54.2
        52.4
        7.6
        ph65_ogr_R1_B4
        59.7
        57.8
        52.4
        8.7
        ph65_ogr_R2_B1
        57.2
        53.8
        52.4
        7.4
        ph65_ogr_R2_B2
        56.2
        53.4
        52.4
        6.7
        ph65_ogr_R2_B3
        56.8
        53.6
        52.4
        7.2
        ph65_ogr_R2_B4
        56.9
        53.8
        52.4
        7.5
        ph65_ogr_R3_B1
        55.7
        53.2
        52.4
        6.3
        ph65_ogr_R3_B2
        56.2
        53.4
        52.4
        6.7
        ph65_ogr_R3_B3
        56.4
        53.4
        52.4
        6.8
        ph65_ogr_R3_B4
        57.6
        54.6
        52.4
        7.6
        ph6_R1_B1
        56.6
        53.6
        52.4
        7.0
        ph6_R1_B2
        56.7
        53.6
        52.4
        7.1
        ph6_R1_B3
        56.8
        53.6
        52.4
        7.1
        ph6_R1_B4
        62.4
        61.6
        52.4
        9.2
        ph6_R2_B1
        58.1
        54.4
        52.4
        7.8
        ph6_R2_B2
        56.9
        53.6
        52.4
        7.1
        ph6_R2_B3
        57.1
        53.8
        52.4
        7.4
        ph6_R2_B4
        57.5
        54.6
        52.4
        8.1
        ph6_R3_B1
        60.1
        57.6
        52.0
        8.5
        ph6_R3_B2
        59.0
        55.8
        52.4
        8.2
        ph6_R3_B3
        55.1
        53.0
        52.4
        5.8
        ph6_R3_B4
        56.2
        53.4
        52.4
        6.8
        ph6_ogr_R1_B1
        55.9
        53.2
        52.4
        6.5
        ph6_ogr_R1_B2
        56.2
        53.4
        52.4
        6.7
        ph6_ogr_R1_B3
        56.5
        53.4
        52.4
        7.0
        ph6_ogr_R1_B4
        56.2
        53.4
        52.4
        6.9
        ph6_ogr_R2_B1
        57.7
        54.0
        52.4
        7.7
        ph6_ogr_R2_B2
        57.0
        53.6
        52.4
        7.3
        ph6_ogr_R2_B3
        56.7
        53.6
        52.4
        7.1
        ph6_ogr_R2_B4
        56.9
        53.6
        52.4
        7.2
        ph6_ogr_R3_B1
        56.4
        53.4
        52.4
        6.8
        ph6_ogr_R3_B3
        57.3
        53.8
        52.4
        7.4
        ph6_ogr_R3_B4
        56.5
        53.4
        52.4
        6.9
        surface_R1_B1
        55.3
        53.0
        52.4
        5.9
        surface_R1_B2
        56.0
        53.4
        52.4
        6.5
        surface_R1_B3
        55.9
        53.2
        52.4
        6.4
        surface_R1_B4
        55.3
        53.0
        52.4
        6.0
        surface_R2_B1
        57.2
        53.8
        52.4
        7.5
        surface_R2_B2
        57.7
        54.2
        52.4
        7.8
        surface_R2_B3
        56.0
        53.2
        52.4
        6.6
        surface_R2_B4
        55.8
        53.2
        52.4
        6.4
        surface_R3_B1
        55.9
        53.2
        52.4
        6.5
        surface_R3_B2
        58.6
        55.0
        52.4
        8.0
        surface_R3_B4
        60.0
        56.8
        52.4
        8.6

        Base composition

        Base composition histogram by position (bhist). The plot shows the percentage of G+C, A+T, and N bases for each position in the reads.

        Relative composition

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        Version: 0.12.1

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        All samples have sequences of a single length (250bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceSamplesOccurrences% of all reads
        GTTCTACATCTGCTCCCTTCCCTTTTGGCTGCAGTACGTCCTCCAGCATG
        166
        17939525
        0.9045%
        GTCTTATACTTGGGTTTGTCTGGTCAACCACCGCGGTCTCCGTCGTCAGG
        166
        13875976
        0.6996%
        GCCCTGGGGACGTCGTCGCGGGTGGCTAAGCGCACCGTGGGCTTGTACTC
        166
        12305410
        0.6204%
        ATGTAGAACAGGTCTGCCACTGTCAGGTTGCACAAGTACACTCCCAACTC
        166
        12261649
        0.6182%
        ACCCTATTCAAGCCTGGCAGCGAGCTATCAATTACTACAGATTTCTCGTG
        166
        10780616
        0.5435%
        CTTCTGACCAGCAGCAACACATGATATGGCAGGAAGCACGCGAGGAAAAT
        166
        10695012
        0.5392%
        GAATAGGGTAGTGCTCGAAGCAGACCCTGTGCTGATTCTCGTCCTCGATC
        166
        10013724
        0.5049%
        GAGCTACATCTTCTGCCTGGTATTCGCCGACTACAAGGACGATGATGACG
        166
        9148780
        0.4613%
        GGTCAGAAGCGTGTGGGAGGCATCTTGTGACTTCGCCAAGGGAGTCTTTA
        166
        8156703
        0.4112%
        GTGCTGAGCACAAGTCTCTGAATTTGGTCTTTGCGAGATTTCTGAGTACC
        166
        8144354
        0.4106%
        ATCCACCAGACCCTCGCTCCCGTGGTTTACGTTACGGTACTTGTCGTAGG
        166
        7476585
        0.3770%
        AAGCAGACCCTGTGCTGATTCTCGTCCTCGATCACTTCCTCGTGCATCAA
        166
        7291043
        0.3676%
        GTATATATTCTCATAAAGAAGAATCCCGCACACTTGGCAGCTCAGGTCAC
        166
        7566169
        0.3815%
        AGCGTGGACCGCTACCTGGCCGTAGCCCATCCTTTCCGATTCCACCAGTT
        166
        7262512
        0.3662%
        GTCCTGGATTTTCCTCCACATCACCAGCTTGTTTCAGTAGACTAAAATTA
        166
        6923353
        0.3491%
        CTACAAGGACGATGATGACGCCAGCATCGATATGGGGAACATCACTGCCG
        166
        6670813
        0.3363%
        CCTCTGGGGCACCCAGCGGATATGCTTCGCGTGCCCTGCCGGTCCTTGAA
        166
        7196386
        0.3628%
        CCATGAAGACGATCATCGCCCTGAGCTACATCTTCTGCCTGGTATTCGCC
        166
        6755794
        0.3406%
        GATTATACCGCAACTACACGCCACCCCGTCAGATCCGGCCACCATGAAGA
        166
        6619857
        0.3338%
        GCGTTAAAGACTCCCTTGGCGAAGTCACAAGATGCCTCCCACACGCTTCT
        166
        6476300
        0.3265%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1